Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001681.1 Hibiscus syriacus cultivar Beakdansim tig00003359_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 140752
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 2
Found at i:116439 original size:20 final size:21
Alignment explanation
Indices: 116411--116449 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
116401 AAAATGTATA
*
116411 TTATATATTTTTA-TATTTAT
1 TTATATATTATTATTATTTAT
*
116431 TTATTTATTATTATTATTT
1 TTATATATTATTATTATTT
116450 TGATTACTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (21 bp):
TTATATATTATTATTATTTAT
Found at i:116461 original size:30 final size:31
Alignment explanation
Indices: 116409--116467 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
116399 TAAAAATGTA
* *
116409 TATTATATATTTTTATATTTA-TTTATTTAT
1 TATTATATATTTTGATACTTATTTTATTTAT
116439 TATTAT-TATTTTGATTACTTATTTTATTT
1 TATTATATATTTTGA-TACTTATTTTATTT
116468 TATTTTTTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.28
30 11 0.44
31 7 0.28
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (31 bp):
TATTATATATTTTGATACTTATTTTATTTAT
Found at i:117297 original size:20 final size:22
Alignment explanation
Indices: 117268--117311 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
117258 ACAAGGAAAG
*
117268 TCACCGAAG-ACCG-AAAGGTC
1 TCACCAAAGAACCGTAAAGGTC
*
117288 TCACCAAAGAACGGTAAAGGTC
1 TCACCAAAGAACCGTAAAGGTC
117310 TC
1 TC
117312 GCCTTTCTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 3 0.15
22 9 0.45
ACGTcount: A:0.36, C:0.27, G:0.23, T:0.14
Consensus pattern (22 bp):
TCACCAAAGAACCGTAAAGGTC
Found at i:117842 original size:19 final size:20
Alignment explanation
Indices: 117826--117862 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
117816 ATTTTTTTTT
*
117826 ATTTTTTTTC-TTATTTTGG
1 ATTTTTTTACTTTATTTTGG
117845 ATTTTTTTACTTTATTTT
1 ATTTTTTTACTTTATTTT
117863 CATTATCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.76
Consensus pattern (20 bp):
ATTTTTTTACTTTATTTTGG
Found at i:118086 original size:31 final size:30
Alignment explanation
Indices: 118020--118086 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
118010 AGTATTTTAT
*
118020 TTATCTATTATTATTTTTTATTTGTTCTTG
1 TTATCTATTAATATTTTTTATTTGTTCTTG
*
118050 -GATCTATTAAATATTTATTTATTTGTT-TTG
1 TTATCTATT-AATATTT-TTTATTTGTTCTTG
118080 TTATCTA
1 TTATCTA
118087 ACATTTGCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 7 0.23
30 9 0.29
31 15 0.48
ACGTcount: A:0.22, C:0.06, G:0.07, T:0.64
Consensus pattern (30 bp):
TTATCTATTAATATTTTTTATTTGTTCTTG
Found at i:118438 original size:6 final size:6
Alignment explanation
Indices: 118427--118459 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
118417 GAGATGGATA
118427 TTCATC TTCATC TTCATC TTCATC TTCATC TTC
1 TTCATC TTCATC TTCATC TTCATC TTCATC TTC
118460 TGGCTCTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.33, G:0.00, T:0.52
Consensus pattern (6 bp):
TTCATC
Found at i:118874 original size:3 final size:3
Alignment explanation
Indices: 118868--118980 Score: 190
Period size: 3 Copynumber: 37.7 Consensus size: 3
118858 TTTTTATCCA
* *
118868 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
118916 TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
118964 TAT TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
118981 AATATATTAA
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 102 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:119020 original size:20 final size:19
Alignment explanation
Indices: 118979--119023 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
118969 CTATTATTAT
* *
118979 TAAATATATTAAATACATA
1 TAAATATATTAAAAACAAA
*
118998 TAAATATTATTAAAAATAAA
1 TAAATA-TATTAAAAACAAA
119018 TAAATA
1 TAAATA
119024 ATAAAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAATATATTAAAAACAAA
Found at i:120409 original size:19 final size:19
Alignment explanation
Indices: 120371--120408 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
120361 TGTAATTTAG
120371 TCATTTATTTTATATGTTT
1 TCATTTATTTTATATGTTT
120390 TCATTTATTTTAT-TGTTT
1 TCATTTATTTTATATGTTT
120408 T
1 T
120409 TAAATATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (19 bp):
TCATTTATTTTATATGTTT
Found at i:120478 original size:19 final size:20
Alignment explanation
Indices: 120441--120482 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
120431 TTTTTATTTT
120441 TATTTTATTATATGAATAAA
1 TATTTTATTATATGAATAAA
**
120461 TATTTTA-TATATTCATAAA
1 TATTTTATTATATGAATAAA
120480 TAT
1 TAT
120483 ATATAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
TATTTTATTATATGAATAAA
Found at i:121249 original size:13 final size:15
Alignment explanation
Indices: 121218--121254 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
121208 TTATATGTTT
121218 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
121233 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
121246 TA-TTTATTT
1 TATTTTATTT
121255 TTATGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:131850 original size:12 final size:11
Alignment explanation
Indices: 131830--131911 Score: 60
Period size: 11 Copynumber: 7.2 Consensus size: 11
131820 ATTATGCTTG
*
131830 AAGAGAAAAAAG
1 AAGA-AAAAAAA
131842 AAGAAAAAAAA
1 AAGAAAAAAAA
*
131853 AA-AAATAGAAA
1 AAGAAA-AAAAA
*
131864 ATGAAAAAGAAA
1 AAGAAAAA-AAA
* *
131876 AA-AAAAAGAG
1 AAGAAAAAAAA
131886 AAGAAAAAAAA
1 AAGAAAAAAAA
131897 AAGGAAAAAAGAA
1 AA-GAAAAAA-AA
131910 AA
1 AA
131912 AGGGGGTCAA
Statistics
Matches: 55, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
10 6 0.11
11 27 0.49
12 18 0.33
13 4 0.07
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:131856 original size:16 final size:16
Alignment explanation
Indices: 131835--131912 Score: 58
Period size: 16 Copynumber: 4.9 Consensus size: 16
131825 GCTTGAAGAG
131835 AAAAAAGAAGAAAAAA
1 AAAAAAGAAGAAAAAA
*
131851 AAAAAA-ATAG-AAAAT
1 AAAAAAGA-AGAAAAAA
*
131866 GAAAAAGAA-AAAAAA
1 AAAAAAGAAGAAAAAA
*
131881 AAGAGAAGAA-AAAAAA
1 AA-AAAAGAAGAAAAAA
131897 AAGGAAAA-AAGAAAAA
1 AA--AAAAGAAGAAAAA
131913 GGGGGTCAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
15 16 0.32
16 25 0.50
17 9 0.18
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (16 bp):
AAAAAAGAAGAAAAAA
Found at i:131882 original size:28 final size:26
Alignment explanation
Indices: 131830--131912 Score: 85
Period size: 28 Copynumber: 3.0 Consensus size: 26
131820 ATTATGCTTG
*
131830 AAGAGAAAAAAGAAGAAAAAAAAAAAA
1 AAGA-AAAAAAAAAGAAAAAAAAAAAA
* *
131857 ATAGAAAATGAAAAAGAAAAAAAAAAGAG
1 A-AGAAAA-AAAAAAGAAAAAAAAAA-AA
* *
131886 AAGAAAAAAAAAAGGAAAAAAGAAAA
1 AAGAAAAAAAAAAGAAAAAAAAAAAA
131912 A
1 A
131913 GGGGGTCAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
26 2 0.04
27 18 0.39
28 24 0.52
29 2 0.04
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (26 bp):
AAGAAAAAAAAAAGAAAAAAAAAAAA
Found at i:131911 original size:13 final size:12
Alignment explanation
Indices: 131837--131911 Score: 70
Period size: 12 Copynumber: 6.3 Consensus size: 12
131827 TTGAAGAGAA
131837 AAAAGAAGAAAA-
1 AAAAGAA-AAAAG
131849 AAAA-AAAAATAG
1 AAAAGAAAAA-AG
131861 AAAATG-AAAAAG
1 AAAA-GAAAAAAG
131873 AAAA-AAAAAAG
1 AAAAGAAAAAAG
*
131884 AGAAGAAAAAA-
1 AAAAGAAAAAAG
131895 AAAAGGAAAAAAG
1 AAAA-GAAAAAAG
131908 AAAA
1 AAAA
131912 AGGGGGTCAA
Statistics
Matches: 53, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
10 3 0.06
11 15 0.28
12 27 0.51
13 8 0.15
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.03
Consensus pattern (12 bp):
AAAAGAAAAAAG
Found at i:131911 original size:41 final size:42
Alignment explanation
Indices: 131835--131913 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 42
131825 GCTTGAAGAG
* *
131835 AAAAAAGAAGAAAAAAAAAAAAATAGAAAATGAAAAAGAAAA
1 AAAAAAGAAGAAAAAAAAAAAAAGAGAAAAAGAAAAAGAAAA
*
131877 AAAAAAG-AGAAGAAAAAAAAAAG-GAAAAAAGAAAAAG
1 AAAAAAGAAGAAAAAAAAAAAAAGAG-AAAAAGAAAAAG
131914 GGGGTCAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 1 0.03
41 25 0.76
42 7 0.21
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (42 bp):
AAAAAAGAAGAAAAAAAAAAAAAGAGAAAAAGAAAAAGAAAA
Found at i:133106 original size:83 final size:83
Alignment explanation
Indices: 132996--133644 Score: 1031
Period size: 83 Copynumber: 7.9 Consensus size: 83
132986 ATATCCCAGT
*
132996 CCAAGCATTGAA--TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
*
133059 TGACCTGGTTTAACAGAA
66 TGATCTGGTTTAACAGAA
133077 CCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
* * *
133142 TGACCTGGTTTAGCAG-T
66 TGATCTGGTTTAACAGAA
* *
133159 CCAAGCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATT
1 CCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
*
133224 TGATCTGATTTAACAGAA
66 TGATCTGGTTTAACAGAA
133242 CCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
*
133307 TGACCTGGTTTAACAGAA
66 TGATCTGGTTTAACAGAA
* *
133325 CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATT
1 CCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
* *
133390 TGATCT-GATTATATAGAA
66 TGATCTGGTTTA-ACAGAA
* *
133408 TCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATT
1 CCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
* *
133473 TGATCT-GATTATATAGAA
66 TGATCTGGTTTA-ACAGAA
* *
133491 CCAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
* **
133556 TGATTTGGTTGGACAGAA
66 TGATCTGGTTTAACAGAA
*
133574 -CAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATT
1 CCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
133638 TGATCTG
66 TGATCTG
133645 AAGAAGTGCA
Statistics
Matches: 530, Mismatches: 33, Indels: 9
0.93 0.06 0.02
Matches are distributed among these distances:
81 11 0.02
82 147 0.28
83 370 0.70
84 2 0.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.37
Consensus pattern (83 bp):
CCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGGTTTAACAGAA
Found at i:134359 original size:111 final size:111
Alignment explanation
Indices: 134202--134660 Score: 793
Period size: 111 Copynumber: 4.2 Consensus size: 111
134192 GATTCAAATC
* *
134202 CATCATTTGATGGATCA-TTTGCCAGAGAAGTTCATAATGAGAAGAACTCAT-TGAAGAAGGAAG
1 CATCATTTGATGGATCATTTTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
*
134265 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
66 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
* *
134311 CATCATTTGGTGGATCATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 CATCATTTGATGGATCAT-TTTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
134376 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
65 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
*
134423 CATCACTTGATGGATCATTTTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
1 CATCATTTGATGGATCATTTTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
134488 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
66 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
*
134534 CATCACTTGATGGATCATTTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCA-TTTTTCCAG-AAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
134599 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT---TGAATT
64 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
134644 CATCATTTGATGGATCA
1 CATCATTTGATGGATCA
134661 ACATTGCCAG
Statistics
Matches: 338, Mismatches: 7, Indels: 9
0.95 0.02 0.03
Matches are distributed among these distances:
109 16 0.05
110 22 0.07
111 142 0.42
112 82 0.24
113 76 0.22
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (111 bp):
CATCATTTGATGGATCATTTTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
Found at i:134637 original size:224 final size:218
Alignment explanation
Indices: 134202--134660 Score: 792
Period size: 223 Copynumber: 2.1 Consensus size: 218
134192 GATTCAAATC
*
134202 CATCATTTGATGGATCATTTGCCAGAGAAGTTCATAATGAGAAGAACTCATTGAAGAAGGAAGAA
1 CATCATTTGATGGATCATTTGCCAGAAAAGTTCATAATGAGAAGAACTCATTGAAGAAGGAAGAA
* *
134267 GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGGATCATCTT
66 GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCACTTGATGGATCATCTT
*
134332 TTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
131 TTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
134397 AATTTGTTCAACCTTTTACCTGAATT
196 AATTTGTTCAACCTTTT---TGAATT
* *
134423 CATCACTTGATGGATCATTTTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
1 CATCATTTGATGGATCA-TTTGCCAGAAAAGTTCATAATGAGAAGAACTCAT-TGAAGAAGGAAG
* *
134488 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATCATT
64 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCACTTGATGGATCATC
134553 TTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
129 TTTTCCAG-AAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
134618 AAGAATTTGTTCAACCTTTTTGAATT
193 AAGAATTTGTTCAACCTTTTTGAATT
134644 CATCATTTGATGGATCA
1 CATCATTTGATGGATCA
134661 ACATTGCCAG
Statistics
Matches: 226, Mismatches: 9, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
221 38 0.17
222 32 0.14
223 81 0.36
224 75 0.33
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (218 bp):
CATCATTTGATGGATCATTTGCCAGAAAAGTTCATAATGAGAAGAACTCATTGAAGAAGGAAGAA
GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCACTTGATGGATCATCTT
TTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
AATTTGTTCAACCTTTTTGAATT
Found at i:134726 original size:271 final size:265
Alignment explanation
Indices: 134410--134902 Score: 844
Period size: 266 Copynumber: 1.8 Consensus size: 265
134400 TTGTTCAACC
134410 TTTTACCTGAATTCATCACTTGATGGATCATTTTTCCAGAAAAGTTCATAATGAGAAGAACTCAT
1 TTTTACCTGAATTCATCACTTGATGGATCATTTTTCCAGAAAAGTTCATAATGAGAAGAACTCAT
*
134475 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAC
66 CTGAAGAA-G--GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAA-TCATCAA
* *
134540 TTGATGGATCATTTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
127 TTGATGGATCATCTTTTCC-GAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGA
* *
134605 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTTGAATTCATCATTTGATGGATCAACATTGCCA
191 AGTTCATAATAAGAAGAACTTGTTCAA-CTTTTTGAATTCATCATTTGATGGATCAACATTGCCA
134670 GGTAGAGTTCA
255 GGTAGAGTTCA
134681 TTTTACCTGAATTCATCACTTGATGGATCA-TTTTCCAGAAAAAGTTCATAATGAGAAGAACTCA
1 TTTTACCTGAATTCATCACTTGATGGATCATTTTTCCAG-AAAAGTTCATAATGAGAAGAACTCA
134745 TCTGAAGAAGGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCATCAATTG
65 TCTGAAGAAGGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCATCAATTG
* * *
134810 ATGGATTATCTTTTCCGGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTT
130 ATGGATCATCTTTTCCGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTT
134875 CATAATAAGAAGAACTTGTTCAACTTTT
195 CATAATAAGAAGAACTTGTTCAACTTTT
134903 GGCATAATTC
Statistics
Matches: 213, Mismatches: 8, Indels: 8
0.93 0.03 0.03
Matches are distributed among these distances:
265 5 0.02
266 67 0.31
267 23 0.11
268 45 0.21
270 9 0.04
271 64 0.30
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (265 bp):
TTTTACCTGAATTCATCACTTGATGGATCATTTTTCCAGAAAAGTTCATAATGAGAAGAACTCAT
CTGAAGAAGGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCATCAATTGA
TGGATCATCTTTTCCGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTC
ATAATAAGAAGAACTTGTTCAACTTTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGA
GTTCA
Found at i:134744 original size:158 final size:156
Alignment explanation
Indices: 134521--134815 Score: 504
Period size: 158 Copynumber: 1.9 Consensus size: 156
134511 TTGTTCAACC
134521 TTTTACCTGAATTCATCACTTGATGGATCATTTTTTCCAGAAAAAGTTCATAATGAGAAGAACTC
1 TTTTACCTGAATTCATCACTTGATGGATCA-TTTTTCCAGAAAAAGTTCATAATGAGAAGAACTC
*
134586 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-TGAATTCATCAT
65 ATCTGAAGAA-G--GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTCTGAA-TCATCAA
134650 TTGATGGATCAACATTGCCAGGTAGAGTTCA
126 TTGATGGATCAACATTGCCAGGTAGAGTTCA
134681 TTTTACCTGAATTCATCACTTGATGGATCA-TTTTCCAGAAAAAGTTCATAATGAGAAGAACTCA
1 TTTTACCTGAATTCATCACTTGATGGATCATTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCA
134745 TCTGAAGAAGGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCATCAATTG
66 TCTGAAGAAGGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT--CTGAATCATCAATTG
134810 ATGGAT
129 ATGGAT
134816 TATCTTTTCC
Statistics
Matches: 131, Mismatches: 1, Indels: 9
0.93 0.01 0.06
Matches are distributed among these distances:
155 38 0.29
157 16 0.12
158 47 0.36
160 30 0.23
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Consensus pattern (156 bp):
TTTTACCTGAATTCATCACTTGATGGATCATTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCA
TCTGAAGAAGGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTCTGAATCATCAATTGAT
GGATCAACATTGCCAGGTAGAGTTCA
Found at i:134885 original size:108 final size:106
Alignment explanation
Indices: 134681--134902 Score: 297
Period size: 108 Copynumber: 2.0 Consensus size: 106
134671 GTAGAGTTCA
*
134681 TTTTACCTGAATTCATCACTTGATGGATCATTTTCCAGAAAAAGTTCATAATGAGAAGAACTCAT
1 TTTTACCTGAATTCATCAATTGATGGATCATTTTCCAGAAAAAGTTCATAATGAGAAGAACTCAT
134746 CTGAAGAAGGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC
66 CTGAAGAAGGAAGAAGTTCATAAT--GAAGAATTTGTTCAACC
* * *
134789 TTTTACCTGAA-TCATCAATTGATGGATTATCTTTTCC-GGAGAAGTTCATAATGAGAAGAACTC
1 TTTTACCTGAATTCATCAATTGATGGATCA--TTTTCCAGAAAAAGTTCATAATGAGAAGAACTC
*
134852 ATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA-C
64 ATCTGAAGAAG---GAAGAAGTTCATAAT--GAAGAATTTGTTCAACC
134899 TTTT
1 TTTT
134903 GGCATAATTC
Statistics
Matches: 103, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
107 16 0.16
108 46 0.45
109 6 0.06
110 5 0.05
111 30 0.29
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.31
Consensus pattern (106 bp):
TTTTACCTGAATTCATCAATTGATGGATCATTTTCCAGAAAAAGTTCATAATGAGAAGAACTCAT
CTGAAGAAGGAAGAAGTTCATAATGAAGAATTTGTTCAACC
Found at i:135226 original size:3 final size:3
Alignment explanation
Indices: 135220--135316 Score: 162
Period size: 3 Copynumber: 33.0 Consensus size: 3
135210 TTTTTATCCA
*
135220 TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
135267 CAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
135314 TAT
1 TAT
135317 ATTTATATAA
Statistics
Matches: 88, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
2 4 0.05
3 84 0.95
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:135370 original size:17 final size:18
Alignment explanation
Indices: 135325--135370 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
135315 ATATTTATAT
* *
135325 AAATACATATATATATTAA
1 AAATA-ATATAAATAATAA
135344 AAATAA-ATAAATAATAA
1 AAATAATATAAATAATAA
135361 AAA-AATATAA
1 AAATAATATAA
135371 TTACAGGCCC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 2 0.08
17 16 0.67
18 1 0.04
19 5 0.21
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (18 bp):
AAATAATATAAATAATAA
Found at i:136719 original size:18 final size:19
Alignment explanation
Indices: 136682--136719 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
136672 TGTAATTTAG
136682 TCATTTATTTTATATGTTT
1 TCATTTATTTTATATGTTT
136701 TCATTTATTTTAT-TGTTT
1 TCATTTATTTTATATGTTT
136719 T
1 T
136720 AAATATATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (19 bp):
TCATTTATTTTATATGTTT
Found at i:136728 original size:19 final size:19
Alignment explanation
Indices: 136687--136728 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
136677 TTTAGTCATT
* *
136687 TATTTTATATGTTTTCATT
1 TATTTTATATGTTTTAATA
136706 TATTTTAT-TGTTTTAAATA
1 TATTTTATATGTTTT-AATA
136725 TATT
1 TATT
136729 GTTTTAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (19 bp):
TATTTTATATGTTTTAATA
Found at i:136737 original size:13 final size:15
Alignment explanation
Indices: 136711--136746 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
136701 TCATTTATTT
136711 TATTGTTTTAAATA-
1 TATTGTTTTAAATAG
136725 TATTGTTTT-AATAG
1 TATTGTTTTAAATAG
136739 TATT-TTTT
1 TATTGTTTT
136747 TTTATTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (15 bp):
TATTGTTTTAAATAG
Found at i:136776 original size:20 final size:20
Alignment explanation
Indices: 136751--136790 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
136741 TTTTTTTTTA
*
136751 TTTTATTTATGAATAAATAT
1 TTTTATATATGAATAAATAT
**
136771 TTTTATATATTCATAAATAT
1 TTTTATATATGAATAAATAT
136791 ATATAATAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTTATATATGAATAAATAT
Found at i:137615 original size:14 final size:15
Alignment explanation
Indices: 137596--137625 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
137586 TACAATTAAA
137596 TTTTAAAAATA-TTT
1 TTTTAAAAATACTTT
137610 TTTTAAAAATACTTT
1 TTTTAAAAATACTTT
137625 T
1 T
137626 AAATTATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTTAAAAATACTTT
Found at i:138749 original size:3 final size:3
Alignment explanation
Indices: 138741--138765 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
138731 ATATATAAAA
138741 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
138766 GTTAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Done.